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Zhang M, Huang W, Zhang L, Feng Z, Zuo Y, Xie Z, Xing W. Nitrite-dependent anaerobic methane oxidation (N-DAMO) in global aquatic environments: A review. Sci Total Environ 2024; 921:171081. [PMID: 38387583 DOI: 10.1016/j.scitotenv.2024.171081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
The vast majority of processes in the carbon and nitrogen cycles are driven by microorganisms. The nitrite-dependent anaerobic oxidation of methane (N-DAMO) process links carbon and nitrogen cycles, offering a novel approach for the simultaneous reduction of methane emissions and nitrite pollution. However, there is currently no comprehensive summary of the current status of the N-DAMO process in natural aquatic environments. Therefore, our study aims to fill this knowledge gap by conducting a comprehensive review of the global research trends in N-DAMO processes in various aquatic environments (excluding artificial bioreactors). Our review mainly focused on molecular identification, global study sites, and their interactions with other elemental cycling processes. Furthermore, we performed a data integration analysis to unveil the effects of key environmental factors on the abundance of N-DAMO bacteria and the rate of N-DAMO process. By combining the findings from the literature review and data integration analysis, we proposed future research perspectives on N-DAMO processes in global aquatic environments. Our overarching goal is to advance the understanding of the N-DAMO process and its role in synergistically reducing carbon emissions and removing nitrogen. By doing so, we aim to make a significant contribution to the timely achievement of China's carbon peak and carbon neutrality targets.
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Affiliation(s)
- Miao Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wenmin Huang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan 430074, China
| | - Lei Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zixuan Feng
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yanxia Zuo
- Analysis and Testing Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zuoming Xie
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Wei Xing
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan 430074, China.
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Nie WB, Xie GJ, Tan X, Ding J, Lu Y, Chen Y, Yang C, He Q, Liu BF, Xing D, Ren N. Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation. Environ Sci Technol 2023; 57:7029-7040. [PMID: 37041123 DOI: 10.1021/acs.est.2c08094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO2-) and inhibition thresholds (0.932 mM vs 2.450 mM NO2-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.
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Affiliation(s)
- Wen-Bo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yi Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Chun Yang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Qiang He
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
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Xu S, Lu W, Muhammad FM, Liu Y, Guo H, Meng R, Wang H. New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches. J Environ Sci (China) 2018; 65:367-374. [PMID: 29548408 DOI: 10.1016/j.jes.2017.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/22/2017] [Accepted: 04/19/2017] [Indexed: 06/08/2023]
Abstract
The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (p<0.05). The redundancy analysis further revealed that the pH, volatile solid and nitrite nitrogen were the most important factors in shaping the NC10 bacterial structure (p=0.01) based on the variation inflation factors selection and Monte Carlo test (999 times). Results of this study extended the existing molecular tools for studying the NC10 bacterial community structures and provided new information on the ecological distributions of NC10 bacteria.
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Affiliation(s)
- Sai Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China.
| | | | - Yanting Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanwen Guo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruihong Meng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongtao Wang
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China
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Chen S, Chen J, Chang S, Yi H, Huang D, Xie S, Guo Q. Aerobic and anaerobic methanotrophic communities in urban landscape wetland. Appl Microbiol Biotechnol 2018; 102:433-45. [PMID: 29079862 DOI: 10.1007/s00253-017-8592-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 01/10/2023]
Abstract
Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) organisms can be important methane sinks in a wetland. However, the influences of the vegetation type on aerobic MOB and n-damo communities in wetland, especially in constructed wetland, remain poorly understood. The present study investigated the influences of the vegetation type on both aerobic MOB and n-damo organisms in a constructed urban landscape wetland. Sediments were collected from eight sites vegetated with different plant species. The abundance (1.19-3.27 × 107 pmoA gene copies per gram dry sediment), richness (Chao1 estimator = 16.3-81.5), diversity (Shannon index = 2.10-3.15), and structure of the sediment aerobic MOB community were found to vary considerably with sampling site. In contrast, n-damo community abundance (8.74 × 105-4.80 × 106 NC10 16S rRNA gene copies per gram dry sediment) changed slightly with the sampling site. The richness (Chao1 estimator = 1-11), diversity (Shannon index = 0-0.78), and structure of the NC10 16S rRNA gene-based n-damo community illustrated slight site-related changes, while the spatial changes of the pmoA gene-based n-damo community richness (Chao1 estimator = 1-8), diversity (Shannon index = 0-0.99), and structure were considerable. The vegetation type could have a profound impact on the wetland aerobic MOB community and had a stronger influence on the pmoA-based n-damo community than on the NC10 16S-based one in urban wetland. Moreover, the aerobic MOB community had greater abundance and higher richness and diversity than the n-damo community. Methylocystis (type II MOB) predominated in urban wetland, while no known type I MOB species was detected. In addition, the ratio of total organic carbon to total nitrogen (C/N) might be a determinant of sediment n-damo community diversity and aerobic MOB richness.
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Bhattacharjee AS, Motlagh AM, Jetten MSM, Goel R. Methane dependent denitrification- from ecosystem to laboratory-scale enrichment for engineering applications. Water Res 2016; 99:244-252. [PMID: 27176548 DOI: 10.1016/j.watres.2016.04.070] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/29/2016] [Accepted: 04/30/2016] [Indexed: 05/28/2023]
Abstract
Managing nitrogen and carbon cycles in engineered and natural ecosystems is an environmental challenge. In this manuscript, we report a process which connects these two cycles with immense ecological and engineering significance. Sediments, collected from Jordan River in Salt Lake City, Utah were used as seed to start a laboratory-scale denitrification coupled to anaerobic methane oxidation (n-DAMO) reactor fed with methane (CH4) and nitrite (NO2(-)). Methane (CH4)-dependent denitrification in sediments of a nutrient-impaired river was found to be in the range of 40 nmol kg(-1) d(-1) to 70 nmol kg(-1) d(-1). Post 19 months of operation of the lab scale reactor, the n-DAMO reactor achieved nitrite removal rate of 2.88 mmol L(-1) d(-1). Enrichment of n-DAMO prokaryotes was evident from the increase in 16S rRNA gene copy number of bacteria belonging to the NC10 phylum in the reactor, corroborating with increase in the oxidation rates of CH4 coupled with NO2(-)-N removal from 21 μM to 190 μM of CH4 d(-1). Based on stable isotope experiments by other researchers, nitric oxide dismutase (nod) functional gene was hypothesized to be responsible for splitting nitric oxide to nitrogen and oxygen and this internally generated oxygen is utilized by n-DAMO prokaryotes to oxidize methane gas. Primers targeting the unique nitric oxide dismutase (nod) gene were developed and tested on the enrichment culture for the first time. This revealed that n-DAMO organisms are closely related yet distinct from, the M. oxyfera which had been enriched in earlier studies. The results emphasize tremendous future promise to use these novel organisms for wastewater treatment purposes, especially to take advantage of the dissolved methane present in anaerobic digester effluents.
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Affiliation(s)
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Ramesh Goel
- Civil & Environmental Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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Cui M, Ma A, Qi H, Zhuang X, Zhuang G. Anaerobic oxidation of methane: an "active" microbial process. Microbiologyopen 2015; 4:1-11. [PMID: 25530008 PMCID: PMC4335971 DOI: 10.1002/mbo3.232] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/14/2014] [Accepted: 11/24/2014] [Indexed: 12/01/2022] Open
Abstract
The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. AOM was first found to be coupled with sulfate reduction and mediated by anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). ANME, often forming consortia with SRB, are phylogenetically related to methanogenic archaea. ANME-1 is even able to produce methane. Subsequently, it has been found that AOM can also be coupled with denitrification. The known microbes responsible for this process are Candidatus Methylomirabilis oxyfera (M. oxyfera) and Candidatus Methanoperedens nitroreducens (M. nitroreducens). Candidatus Methylomirabilis oxyfera belongs to the NC10 bacteria, can catalyze nitrite reduction through an "intra-aerobic" pathway, and may catalyze AOM through an aerobic methane oxidation pathway. However, M. nitroreducens, which is affiliated with ANME-2d archaea, may be able to catalyze AOM through the reverse methanogenesis pathway. Moreover, manganese (Mn(4+) ) and iron (Fe(3+) ) can also be used as electron acceptors of AOM. This review summarizes the mechanisms and associated microbes of AOM. It also discusses recent progress in some unclear key issues about AOM, including ANME-1 in hypersaline environments, the effect of oxygen on M. oxyfera, and the relationship of M. nitroreducens with ANME.
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Affiliation(s)
- Mengmeng Cui
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Anzhou Ma
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Hongyan Qi
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
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